6LQS

Cryo-EM structure of 90S small subunit preribosomes in transition states (State D)

  • Classification: RIBOSOME
  • Organism(s): Saccharomyces cerevisiae S288C
  • Mutation(s): No 

  • Deposited: 2020-01-14 Released: 2020-09-16 
  • Deposition Author(s): Du, Y., Ye, K.
  • Funding Organization(s): National Natural Science Foundation of China (NSFC), Chinese Academy of Sciences

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states.

Du, Y.An, W.Zhu, X.Sun, Q.Qi, J.Ye, K.

(2020) Science 369: 1477-1481

  • DOI: 10.1126/science.aba9690
  • Primary Citation of Related Structures:  
    6LQT, 6LQS, 6LQV, 6LQU, 6LQP, 6LQR, 6LQQ

  • PubMed Abstract: 
  • The 90 S preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 S ribosome. Here, we gained insight into this transition by determining cryo-electron microsco ...

    The 90 S preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40 S ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of Saccharomyces cerevisiae intermediates in the path from the 90 S to the pre-40 S The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90 S , driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90 S through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90 S progression.


    Organizational Affiliation

    University of Chinese Academy of Sciences, Beijing 100049, China.



Macromolecules

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S1-ASC255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-ASF261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S5SG225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S6-ASH236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-ASI190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 9
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40S ribosomal protein S8-ASJ200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 10
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40S ribosomal protein S9-ASK197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 11
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40S ribosomal protein S11-ASM156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 12
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40S ribosomal protein S13SO151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 13
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40S ribosomal protein S14-ASP137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 14
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40S ribosomal protein S16-ASR143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 15
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40S ribosomal protein S22-BSX130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22BRPS24BYLR367WL8039.6
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S23-ASY145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 17
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40S ribosomal protein S24-ASZ135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 18
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40S ribosomal protein S27-ASc82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 19
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40S ribosomal protein S28-ASd67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 20
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rRNA 2'-O-methyltransferase fibrillarin3B3C327Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP1LOT3YDL014WD2870
EC: 2.1.1
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Entity ID: 21
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Nucleolar protein 563D504Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP56SIK1YLR197WL8167.9
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Entity ID: 22
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Nucleolar protein 583E511Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP58NOP5YOR310CO6108
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Entity ID: 23
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Ribosomal RNA-processing protein 93F573Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP9YPR137W
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Entity ID: 24
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13 kDa ribonucleoprotein-associated protein3G3H126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SNU13YEL026W
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Entity ID: 25
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U3 small nucleolar RNA-associated protein 4A4776Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP4YDR324C
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Entity ID: 26
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U3 small nucleolar RNA-associated protein 5A5643Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP5YDR398WD9509.17
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 8A8713Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP8YGR128C
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 9A9575Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP9YHR196W
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Entity ID: 29
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U3 small nucleolar RNA-associated protein 10AE1769Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP10YJL109CJ0808
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 15AF513Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP15YMR093WYM9582.18
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetailsImage
NET1-associated nuclear protein 1AG896Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NAN1UTP17YPL126W
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetailsImage
Periodic tryptophan protein 2B1900Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: PWP2UTP1YCR057CYCR55C/YCR57C/YCR58C
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Entity ID: 33
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U3 small nucleolar RNA-associated protein 12B2943Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIP2UTP12YLR129WL3116L9233.1
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Entity ID: 34
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U3 small nucleolar RNA-associated protein 13B3817Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP13YLR222C
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Entity ID: 35
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U3 small nucleolar RNA-associated protein 18B8594Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP18YJL069CHRE594J1098
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Entity ID: 36
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U3 small nucleolar RNA-associated protein 21BE939Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP21YLR409CL8084.22
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetailsImage
U3 small nucleolar RNA-associated protein 6B6440Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP6YDR449CD9461.34
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetailsImage
Bud site selection protein 215B214Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BUD21UTP16YOR078WYOR29-29
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Entity ID: 39
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U3 small nucleolar RNA-associated protein 75C554Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP7KRE31YER082C
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Entity ID: 40
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U3 small nucleolar RNA-associated protein 115D250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP11YKL099CYKL449
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Entity ID: 41
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U3 small nucleolar RNA-associated protein MPP105E593Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP10YJR002WJ1411YJR83.5
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Entity ID: 42
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U3 small nucleolar ribonucleoprotein protein IMP35F183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP3YHR148W
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Entity ID: 43
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U3 small nucleolar ribonucleoprotein protein IMP45G290Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: IMP4YNL075WN2353
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Entity ID: 44
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Something about silencing protein 105H610Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SAS10UTP3YDL153CD1545
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Entity ID: 45
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Protein SOF15I489Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SOF1YLL011WL1339
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Entity ID: 46
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rRNA-processing protein FCF25J217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF2YLR051CL2128
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Entity ID: 47
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rRNA-processing protein FCF15K189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: FCF1YDR339CD9651.9
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Entity ID: 48
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rRNA biogenesis protein RRP5RD1729Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP5FMI1YMR229CYM9959.11C
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Entity ID: 49
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U3 small nucleolar RNA-associated protein 22RE1237Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP22YGR090W
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Entity ID: 50
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Ribosomal RNA-processing protein 7RF297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP7YCL031CYCL184YCL31C
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Entity ID: 51
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Ribosomal RNA small subunit methyltransferase NEP1RGRH252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EMG1NEP1YLR186WL9470.5
EC: 2.1.1.260
Find proteins for Q06287 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
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Ribosome biogenesis protein BMS1RJ1183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: BMS1YPL217C
Find proteins for Q08965 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 53
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RNA 3'-terminal phosphate cyclase-like proteinRK367Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RCL1RTC1YOL010W
Find proteins for Q08096 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 54
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Nucleolar complex protein 14RN810Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOP14UTP2YDL148CD1566
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Entity ID: 55
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Nucleolar complex protein 4RO552Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: NOC4UTP19YPR144C
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Entity ID: 56
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U3 small nucleolar RNA-associated protein 20RP2493Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP20YBL004WYBL0101
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Entity ID: 57
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U3 small nucleolar RNA-associated protein 14RQ899Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: UTP14YML093W
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Entity ID: 58
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Essential nuclear protein 1RS480Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ENP1MEG1YBR247CYBR1635
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Entity ID: 59
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Pno1RT326Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 60
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Regulator of rDNA transcription protein 14RW206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRT14YIL127C
Find proteins for P40470 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
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Unassigned helices 1X1347Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 62
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Unassigned helices 2X2694Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 63
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Exosome complex component RRP45R5305Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP45YDR280WD9954.1
Find proteins for Q05636 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
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Exosome complex component SKI6R1246Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SKI6ECM20RRP41YGR195WG7587
Find proteins for P46948 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
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Exosome complex component RRP43R3394Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP43YCR035CYCR35CYCR522
Find proteins for P25359 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
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Exosome complex component RRP46R6223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP46YGR095C
Find proteins for P53256 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
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Exosome complex component RRP42R2265Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP42YDL111C
Find proteins for Q12277 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
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Exosome complex component MTR3M3250Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR3YGR158CG6676
Find proteins for P48240 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
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Exosome complex component RRP40R0240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP40YOL142W
Find proteins for Q08285 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
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Exosome complex component RRP4r4359Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP4YHR069C
Find proteins for P38792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
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Exosome complex component CSL4C4292Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: CSL4SKI4YNL232WN1154
Find proteins for P53859 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
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Exosome complex exonuclease DIS3R41001Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: DIS3RRP44YOL021CO2197
EC: 3.1.13 (PDB Primary Data), 3.1.26 (PDB Primary Data)
Find proteins for Q08162 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
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Exosome complex exonuclease RRP6r6733Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RRP6UNC733YOR001W
EC: 3.1.13
Find proteins for Q12149 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 74
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Exosome complex protein LRP1R7184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: LRP1RRP47YC1DYHR081W
Find proteins for P38801 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
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ATP-dependent RNA helicase DOB1M41073Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MTR4DOB1YJL050WJ1158
EC: 3.6.4.13
Find proteins for P47047 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
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M-phase phosphoprotein 6 homologM6186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: MPP6YNR024WN3230
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Entity ID: 1
MoleculeChainsLengthOrganismImage
U3 snoRNA3A333Saccharomyces cerevisiae S288C
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5' ETS5A700Saccharomyces cerevisiae S288C
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Entity ID: 3
MoleculeChainsLengthOrganismImage
18S pre-rRNASA1809Saccharomyces cerevisiae S288C
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download CCD File 
RJ
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ZN
Query on ZN

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5K, Sc
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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RJ
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-01-14 
  • Released Date: 2020-09-16 
  • Deposition Author(s): Du, Y., Ye, K.

Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China91940302, 91540201, 31430024, 31325007
Chinese Academy of SciencesChinaXDB08010203

Revision History 

  • Version 1.0: 2020-09-16
    Type: Initial release
  • Version 1.1: 2020-09-30
    Changes: Database references